A federal program in 1998 that allowed a native-only commercial fishery a day ahead of the usual commercial fishing season in B.C. did not violate the charter rights of non-aboriginal fishermen, the Supreme Court of Canada ruled Friday.

The Supreme Court ruling upheld the 2004 convictions of more than 50 non-native B.C. fishermen who took part in a protest fishery during a prohibited period.

On Aug. 19, 1998, the Department of Fisheries and Oceans granted an exclusive communal fishing licence to the Musqueam, Burrard and Tsawwassen bands to fish for salmon in the mouth of the Fraser River for 24 hours in advance of the usual commercial season, and to sell their catch.

"The agreement entered into with the Musqueam, Burrard and Tsawwassen bands expressly stated that it did not create any aboriginal rights," the court said.

In 2003, a B.C. provincial court stayed all the charges against the more than 50 commercial fishermen on the grounds that the special fishing licence granted to the three bands breached the charter rights of non-natives. A year later, the B.C. Supreme Court overturned the decision and the protesters were convicted.

The B.C. Fisheries Survival Coalition appealed the B.C. Supreme Court decision in 2006, but was dismissed by the B.C. Court of Appeal on the grounds that the special fishery licence did not constitute denial of non-native fishermen's rights. The coalition then appealed to the Supreme Court of Canada.

Despite the Supreme Court ruling, the judges identified a "real conflict" over the issue, because non-native fishermen were treated differently based on "racial differences."

"It is established, in this case, that the right given by the Pilot Sales Program is limited to aboriginals and has a detrimental effect on non-aboriginal commercial fishers who operate in the same region as the beneficiaries of the program," the court ruling said.

"It is also clear that the disadvantage is related to racial differences … The right to equality afforded to every individual under Section 15 [of the charter] is not capable of application consistently with the rights of aboriginal fishers holding licences under the Pilot Sales Program. There is a real conflict," it said.

On Friday, Phil Eidsvik, a spokesman for the B.C. Fisheries Survival Coalition, which spearheaded the Supreme Court challenge, said the judges got it wrong.

The "aboriginal only" fisheries opening is still a practice that is unfair to other Canadian citizens, Eidsvik said.

"The proper way to do this if they wanted to increase aboriginal participation would have been what they have been doing in recent years … buy licences and vessels for aboriginal bands, issue them to aboriginal bands and let them fish in the same fishery that I do … We all fish together under the same rules and regulations," Eidsvik said.

Each of the 97 aboriginal bands on the Fraser River will now expect their own exclusive fishing opportunity, he said.

Eidsvik told CBC News Friday that the coalition will make a direct appeal to Prime Minister Stephen Harper on the matter.